SMTL ID : 4r85.2 (3 other biounits)

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 17E: 5-methylcytosine(Non-covalent)

17E.1: 13 residues within 4Å: Chain A: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.314, A:W.314 Hydrogen bonds: A:Q.151, A:Q.151, A:E.212 17E.8: 13 residues within 4Å: Chain B: H.58, L.76, F.149, Q.151, I.178, H.209, E.212, H.241, E.273, D.308, S.309, W.314 Ligands: FE2.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.314, B:W.314 Hydrogen bonds: B:Q.151, B:Q.151, B:E.212, B:E.273 Water bridges: B:E.212, B:E.212 pi-Cation interactions: B:H.209

2 x FE2: FE (II) ION(Non-covalent)

FE2.2: 6 residues within 4Å: Chain A: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.56, A:H.58, A:H.209, A:H.241, A:D.308 FE2.9: 6 residues within 4Å: Chain B: H.56, H.58, H.209, H.241, D.308 Ligands: 17E.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.56, B:H.58, B:H.209, B:H.241, B:D.308

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: P.92, E.93, R.96, A.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.93, A:E.93 GOL.4: 4 residues within 4Å: Chain A: S.254, F.257, R.292, E.295 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.284, A:R.292 Water bridges: A:S.254 GOL.5: 8 residues within 4Å: Chain A: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.185, A:R.219 Water bridges: A:Q.217, A:E.222 GOL.6: 5 residues within 4Å: Chain A: Q.145, D.173, L.205, L.356, C.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.145, A:C.357 Water bridges: A:L.205 GOL.7: 6 residues within 4Å: Chain A: R.324, D.327, A.328, H.331 Chain B: D.327, A.328 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.327, B:D.327, A:D.327 GOL.10: 8 residues within 4Å: Chain B: R.185, V.189, Q.217, S.218, R.219, F.220, E.222, V.223 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.185, B:R.219, B:E.222 Water bridges: B:Q.217, B:E.222 GOL.11: 5 residues within 4Å: Chain A: W.284 Chain B: S.254, F.257, R.292, E.295 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.292, A:W.284 Water bridges: B:S.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine. To be Published

Release Date

2014-09-17

Peptides

Cytosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Cytosine deaminase

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